Abstract

The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the Iberian Peninsula. The species has recently experienced a strong decline and some of its populations are severely threatened with extinction. To help in the preservation of this species, it is critical to understand its genetic structure and main evolutionary units, as these may have specific local adaptations and could be of great conservation value. Sequencing reduced representation libraries (ddRAD) from 26 specimens selected from across its entire range, we obtained around 45,000 loci per specimen and 1185 single nucleotide polymorphisms. Heterozygosity varied substantially among individuals from different areas. Interestingly, specimens from the southeastern Pyrenees had some of the lowest proportions of heterozygous positions inferred from genome-wide data in mammals so far. In addition, we estimated a tree reflecting genomic divergence, performed a principal component analysis, and carried out a Bayesian analysis of the population structure. Combined evidence supported the existence of five distinct genomic clusters largely coincident with the main mountain ranges where the species occurs, with few specimens presenting relevant admixture levels. There was good correspondence between these populations and the mitochondrial lineages detected in a previous study, yet substantial differences in some areas demonstrate the importance of performing genomic analysis to reveal the whole population history. Although the analysis of further specimens is necessary to better characterize the distribution of the different evolutionary units, the distinctive geographical structure of this species revealed by the genomic data should be considered in future conservation plans.

Keywords

Galemys pyrenaicusddRAD SNPs Conservation genomics Genetic structure

Electronic supplementary material

The online version of this article (doi:10.1007/s10592-016-0865-y) contains supplementary material, which is available to authorized users.

Notes

Acknowledgments

We thank the BTVS-ICNF collection (Banco de Tecidos de Vertebrados Selvagens—Instituto da Conservação da Natureza e das Florestas), Xunta de Galicia, Gobierno de Navarra, Diputación Foral de Gipuzkoa, Gobierno de La Rioja, Parque Nacional de Picos de Europa, Julio Gisbert and Rosa García-Perea (Proyecto Galemia) for Galemys pyrenaicus samples from their respective biological collections, and Henrique Carvalho, Carla Marisa Quaresma and Carlos P. Santos (Instituto da Conservação da Natureza e das Florestas) for their help with the access to the BTVS-ICNF collection. We also thank all the people of the Genomics Core Facility at the Pompeu Fabra University for help with the library preparation and sequencing. This work was financially supported by research Projects CGL2011-22640 and CGL2014-53968-P of the “Plan Nacional I + D+I del Ministerio de Economía y Competitividad” (Spain) to J.C. with contribution of project 014/2008 of the “Convocatoria de ayudas a proyectos de investigación en la Red de Parques Nacionales” (Spain) to J.G. M.Q. was supported by fellowship BES-2012-057135 of the Ministerio de Economía y Competitividad (Spain).